6-78874424-T-G

Position:

• chr6-78874424-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010844.4(IRAK1BP1):​c.315+6533T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,042 control chromosomes in the GnomAD database, including 17,128 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (17128 hom., cov: 33)
• Consequence: IRAK1BP1 NM_001010844.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731

Genes affected

IRAK1BP1 (HGNC:17368): (interleukin 1 receptor associated kinase 1 binding protein 1) Predicted to be involved in I-kappaB kinase/NF-kappaB signaling. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IRAK1BP1	NM_001010844.4	c.315+6533T>G		intron_variant		ENST00000369940.7	NP_001010844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IRAK1BP1	ENST00000369940.7	c.315+6533T>G		intron_variant		1	NM_001010844.4	ENSP00000358956	P1
IRAK1BP1	ENST00000606868.5	c.285+6533T>G		intron_variant, NMD_transcript_variant		1		ENSP00000475570
IRAK1BP1	ENST00000607739.1	c.54+2289T>G		intron_variant		2		ENSP00000475503

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71256 AN: 151924 Hom.: 17118 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.470

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.469 AC: 71283 AN: 152042 Hom.: 17128 Cov.: 33 AF XY: 0.473 AC XY: 35122 AN XY: 74320

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.476

Alfa AF: 0.480 Hom.: 2185

Bravo AF: 0.463

Asia WGS AF: 0.656 AC: 2281 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9352669; hg19: chr6-79584141; COSMIC: COSV64049080;